Following last week’s summary of some student annotation topics, here are some more. I didn’t have time to interview all the students, so some topics were not yet covered, and some only very rapidly, but it gives an idea of … Continue reading →

After 2 weeks of annotation, some of our students presented their preliminary results to the class. Here is a summary. Phosphate and nitrate uptake and metabolism: using KEGG and keywords, the students identified genes to annotate; of these, 45 have … Continue reading →

A new year of the class Sequence a genome with our master students has started! In September, the students cultivated two strains likely to be Pseudomonas protegens, extracted their DNA and prepared it for PacBio sequencing. All of the students … Continue reading →

The students of the Sequence a genome class have been advancing in their analysis of bacterial RNA-seq (see design in previous post). Let’s present here the basic analysis, common to all biological questions which can then be studied using these … Continue reading →

This winter, the Master students preformed the experimental part of our RNA-seq. This blog is a bit late, so they have in the meantime started the bioinformatics analysis, which will be reported in a future blogpost (hopefully less late than … Continue reading →

After a first paper in June last year, a second paper from our class of sequencing, assembling and annotating bacterial genomes with Master students is out: Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students … Continue reading →

After completing genome assembly (see previous blog post), our students have now started 4 sessions of annotation. They have chosen among 15 proposed topics, of interest either for all bacterial genomes, or specifically to this isolate from a solvent-contaminated soil. … Continue reading →

In this first session of the course “Sequence a genome” since we sent DNA to the sequencing facility, we have had the visit of Gerrit Kuhn, who supports PacBio in our area, and who gave a nice presentation of how … Continue reading →

This class has been running since 2010-11, on the following principle: autumn semester: isolate bacterial DNA, sequence using Illumina, assemble; spring semester: close assembly gaps, annotate genome. As anyone following genomics knows, the times they are a’changing again and again, … Continue reading →

The first paper describing a genome sequenced, assembled and annotating by students in our course, which was accepted in April (that blogpost includes the full list of authors with student names in bold), is now online: Comparative genome analysis of … Continue reading →